[Bioperl-l] Bio::SearchIO TFASTX parsing bug
danielmt at fiocruz.br
Tue Oct 19 11:06:57 EDT 2004
we've been using $hit->logical_length('query') on TFASTX reports and
noticed that it corresponds to $result->query_length divided by 3. That
is exactly what we would expect for TBLASTX, where both the query and
hit sequences are translated into aminoacid sequences, however, TFASTX
compares a protein sequence to a DNA sequence database and therefore
just the hit logical length makes sense. So, everything else that
depends on the $hit->logical_length('query') is miscalculated.
We're using bioperl-live from cvs (updated almost daily).
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